[English] 日本語
Yorodumi
- PDB-3dw7: Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dw7
TitleCrystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2656-SeCH3 modified
ComponentsSarcin/Ricin Domain from E. Coli 23 S rRNA
KeywordsRNA / Sarcin Ricin Loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å
AuthorsOlieric, V. / Rieder, U. / Lang, K. / Serganov, A. / Schulze-Briese, C. / Micura, R. / Dumas, P. / Ennifar, E.
CitationJournal: Rna / Year: 2009
Title: A fast selenium derivatization strategy for crystallization and phasing of RNA structures.
Authors: Olieric, V. / Rieder, U. / Lang, K. / Serganov, A. / Schulze-Briese, C. / Micura, R. / Dumas, P. / Ennifar, E.
History
DepositionJul 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sarcin/Ricin Domain from E. Coli 23 S rRNA


Theoretical massNumber of molelcules
Total (without water)8,8211
Polymers8,8211
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.550, 29.550, 76.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

#1: RNA chain Sarcin/Ricin Domain from E. Coli 23 S rRNA


Mass: 8821.242 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.2 M (NH4)2SO4, 50 mM K-MOPS pH 7.0, 10 mM MgCl2, 10 mM MnCl2, vapor diffusion, hanging drop, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2K-MOPS11
3MgCl211
4MnCl211
5H2O11
6(NH4)2SO412
7K-MOPS12
8MgCl212
9MnCl212
10H2O12

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionHighest resolution: 1 Å / Num. obs: 66643 / % possible obs: 95.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 11.643 Å2 / Rsym value: 0.059 / Net I/σ(I): 15.24
Reflection shellResolution: 1→1.1 Å / Mean I/σ(I) obs: 2.5 / Num. measured obs: 47856 / Num. unique obs: 14613 / Rsym value: 0.456 / % possible all: 84.1

-
Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementResolution: 1→20.151 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.1 / σ(F): 1.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.17 3345 5.02 %random
Rwork0.153 ---
obs0.154 66643 95.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.823 Å2 / ksol: 0.454 e/Å3
Displacement parametersBiso max: 46.79 Å2 / Biso mean: 14.405 Å2 / Biso min: 6.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.942 Å2-0 Å20 Å2
2---1.942 Å2-0 Å2
3---0.572 Å2
Refinement stepCycle: LAST / Resolution: 1→20.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 580 0 156 736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004744
X-RAY DIFFRACTIONf_angle_d1.1041166
X-RAY DIFFRACTIONf_chiral_restr0.052152
X-RAY DIFFRACTIONf_plane_restr0.00630
X-RAY DIFFRACTIONf_dihedral_angle_d28.169335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1-1.0140.319830.3061630171359
1.014-1.0290.282940.2632033212773
1.029-1.0460.241250.242355248085
1.046-1.0630.271900.2172586267691
1.063-1.0810.1941130.1932637275097
1.081-1.1010.1481280.1782813294199
1.101-1.1220.1621540.16327482902100
1.122-1.1450.1611390.15727322871100
1.145-1.170.1731610.15427622923100
1.17-1.1970.1821520.15427332885100
1.197-1.2270.1661490.14327752924100
1.227-1.260.1491490.14327652914100
1.26-1.2970.1871240.14727842908100
1.297-1.3390.1791480.14627632911100
1.339-1.3870.171530.14327302883100
1.387-1.4420.1631430.15127192862100
1.442-1.5080.1641440.15727922936100
1.508-1.5870.1561610.14727252886100
1.587-1.6870.1531760.12227142890100
1.687-1.8170.121340.13127932927100
1.817-1.9990.1511570.14327442901100
1.999-2.2880.1931760.1572702287899
2.288-2.8820.1971470.1672716286399
2.882-20.1550.1521450.1352547269293

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more